Protein binding or protein—protein interactions can be broadly defined as the discrete interaction of the surface of one protein with the surface of another protein. Such discrete interaction arises when residues of one protein are proximally located to residues of another protein and attractive forces between the residues such as van der Waals forces, ionic bonds ard hydrogen bonds exist. Specific protein—protein interactions which occur in higher living organisms include, for example, a receptor-binding protein binding to a receptor; a pathogen antigen binding to a host cell receptor and protein interactions at cellular attachment sites.
Proteins and in particular pathogenic proteins such as bacteria, fungi, parasites, and viruses express specific antigens on their surface for interaction. Typically, there are specific sites on antigens, hereinafter referred to as binding epitopes or epitopes, which bind to a complementary portion of a cellular protein called a receptor site.
Identification and/or preparation of compounds, e.g., peptide or polypeptide compounds, that specifically either simulate, that is mimic, or block protein—protein interactions in cells is desirable for a variety of therapeutic and diagnostic purposes and considerable effort has been made to identify protein epitopes. The epitope, in order to be useful in therapeutic and diagnostic fields, needs to be displayed and presented for interaction with other proteins.